From 40f197693d886791ac801db40f28f4e0f0fb805c Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 4 Aug 2011 13:16:16 +0000
Subject: [PATCH] Clustal Omega web service wrapper and tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4462 e3abac25-378b-4346-85de-24260fe3988d
---
 runner/compbio/runner/msa/ClustalO.java |   50 ++++++++++++++++++++++++++++---
 1 file changed, 46 insertions(+), 4 deletions(-)

diff --git a/runner/compbio/runner/msa/ClustalO.java b/runner/compbio/runner/msa/ClustalO.java
index e94dead..ae0d8ec 100644
--- a/runner/compbio/runner/msa/ClustalO.java
+++ b/runner/compbio/runner/msa/ClustalO.java
@@ -26,7 +26,10 @@ import org.apache.log4j.Logger;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.UnknownFileFormatException;
+import compbio.engine.client.CommandBuilder;
+import compbio.engine.client.Executable;
 import compbio.engine.client.SkeletalExecutable;
+import compbio.engine.client.Executable.ExecProvider;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;
 
@@ -34,14 +37,23 @@ public class ClustalO extends SkeletalExecutable<ClustalO> {
 
 	private static Logger log = Logger.getLogger(ClustalO.class);
 	private static final String EXEC_STAT_FILE = "stat.log";
-	private static final String TREE_FILE_EXT = ".dnd";
+	
 
 	public static final String KEY_VALUE_SEPARATOR = "=";
+	
+	/*
+	 * Number of cores parameter name
+	 */
+	private final static String ncorePrm = "--threads";
 
 	/**
-	 * 
-	 * --auto Set options automatically (might overwrite some of your options)
-	 * 
+	 * Number of cores to use, defaults to 1 for local execution or the value of
+	 * "tcoffee.cluster.cpunum" property for cluster execution
+	 */
+	private int ncoreNumber = 0;
+
+	
+	/**
 	 * --threads=<n> Number of processors to use
 	 * 
 	 * -l, --log=<file> Log all non-essential output to this file
@@ -99,5 +111,35 @@ public class ClustalO extends SkeletalExecutable<ClustalO> {
 	public Class<ClustalO> getType() {
 		return (Class<ClustalO>) this.getClass();
 	}
+	
+	@Override
+	public CommandBuilder<ClustalO> getParameters(ExecProvider provider) {
+		// Limit number of cores to 1 for ANY execution which does not set
+		// Ncores explicitly using setNCore method
+		if (ncoreNumber == 0) {
+			setNCore(1);
+		}
+		if (provider == Executable.ExecProvider.Cluster) {
+			int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
+			if (cpunum != 0) {
+				setNCore(cpunum);
+			} 
+		}
+		return super.getParameters(provider);
+	}
+	
+	public void setNCore(int ncoreNumber) {
+		if (ncoreNumber < 1 || ncoreNumber > 100) {
+			throw new IndexOutOfBoundsException(
+					"Number of cores must be within 1 and 100 ");
+		}
+		this.ncoreNumber = ncoreNumber;
+		cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));
+	}
+
+	int getNCore() {
+		return ncoreNumber;
+	}
+
 
 }
-- 
1.7.10.2